One thing you have to learn about STO is, just because it is not in the tooltip doesn't mean it's not there.

Go check your actual cooldowns and you'll see that they indeed get reduced properly. The only exception seems to be Cloaked Tractor Beam Mines where it shows 36 seconds instead of 45 but still gives 45 seconds cooldown. So the only bug beside the tooltip I can see is the tractor beam mine.